[English] 日本語
Yorodumi
- PDB-8tqg: Crystal Structure of Mtb Pks13 Thioesterase domain in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tqg
TitleCrystal Structure of Mtb Pks13 Thioesterase domain in complex with inhibitor X20419
ComponentsPolyketide synthase Pks13
KeywordsBIOSYNTHETIC PROTEIN / polyketide synthase / thioesterase
Function / homology
Function and homology information


DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...: / Thioesterase / Thioesterase domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Polyketide synthase Pks13
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKrieger, I.V. / Sacchettini, J.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI095208 United States
Welch FoundationA-0015 United States
Bill & Melinda Gates FoundationINV-040487 United States
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Inhibitors of the Thioesterase Activity of Mycobacterium tuberculosis Pks13 Discovered Using DNA-Encoded Chemical Library Screening.
Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / ...Authors: Krieger, I.V. / Yalamanchili, S. / Dickson, P. / Engelhart, C.A. / Zimmerman, M.D. / Wood, J. / Clary, E. / Nguyen, J. / Thornton, N. / Centrella, P.A. / Chan, B. / Cuozzo, J.W. / Gengenbacher, M. / Guie, M.A. / Guilinger, J.P. / Bienstock, C. / Hartl, H. / Hupp, C.D. / Jetson, R. / Satoh, T. / Yeoman, J.T.S. / Zhang, Y. / Dartois, V. / Schnappinger, D. / Keefe, A.D. / Sacchettini, J.C.
History
DepositionAug 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polyketide synthase Pks13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5964
Polymers31,7781
Non-polymers8183
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.626, 66.626, 129.953
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw

-
Components

#1: Protein Polyketide synthase Pks13 / Termination polyketide synthase


Mass: 31777.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pks13, Rv3800c / Production host: Escherichia coli (E. coli)
References: UniProt: I6X8D2, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-JR0 / N-benzyl-2-{4-[4-(4,5-dimethoxy-1H-indole-2-carbonyl)piperazine-1-carbonyl]piperidin-1-yl}-6-methylpyrimidine-4-carboxamide


Mass: 625.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H39N7O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.79 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M TRIS-HCL, 2.0-1.8 M AMMONIUM SULFATE, 2%-5% V/V PPG P400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.2→66.63 Å / Num. obs: 15367 / % possible obs: 99 % / Redundancy: 6.2 % / Biso Wilson estimate: 49.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.049 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 2.24 / Num. unique obs: 1295 / CC1/2: 0.598 / Rpim(I) all: 0.931

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.29 Å / SU ML: 0.3911 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.3638
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3129 796 5.2 %RANDOM
Rwork0.2418 14497 --
obs0.2457 15293 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 56 13 2247
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812287
X-RAY DIFFRACTIONf_angle_d1.00793110
X-RAY DIFFRACTIONf_chiral_restr0.0595324
X-RAY DIFFRACTIONf_plane_restr0.0121412
X-RAY DIFFRACTIONf_dihedral_angle_d9.2846331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.44371220.39162352X-RAY DIFFRACTION98.17
2.34-2.520.42071300.3362369X-RAY DIFFRACTION98.7
2.52-2.770.39591140.30732378X-RAY DIFFRACTION97.42
2.77-3.170.38781440.28312388X-RAY DIFFRACTION98.75
3.17-40.31981250.24542428X-RAY DIFFRACTION98.46
4-59.290.26121610.19062582X-RAY DIFFRACTION98.92

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more